Approximations for the Weighted Reversal, Transposition, and Indel Distance Problem with Intergenic Region Information

TL;DR

This paper presents approximation algorithms for calculating genome rearrangement distances involving reversals, transpositions, and indels, considering gene orientations and intergenic region lengths, to improve genome comparison methods.

Contribution

It introduces a novel modeling approach for genomes with gene orientations and intergenic regions, and provides approximation algorithms for the weighted rearrangement distance problem.

Findings

Developed a Labeled Intergenic Breakpoint Graph structure

Provided approximation algorithms with guaranteed bounds

Enhanced genome comparison accuracy

Abstract

Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in intergenic regions, and weights reflecting the expected frequency of each operation. In this article, we model genomes containing at most one copy of each gene by considering gene sequences, with orientations, and representing intergenic regions according to their nucleotide lengths. We looked at a problem called Weighted Reversal, Transposition, and Indel Distance, which seeks the minimal cost sequence composed by the rearrangement operations of reversals, transposition, and indels, capable of transforming one genome into another. We leverage a structure called Labeled Intergenic Breakpoint Graph to show an algorithm for that problem with guaranteed approximations considering some sets of weights for the operations.